Sequence
atgc intronic sequence ATGC exonic sequencegtgagcatcagttcaagtttttgagatttctttggtgtttctgtttttacattgctggtttcttgatggttttaaaatagATGGGAGGCAAGGATGGGCTGAGTTTGCTCCGTATGATGCTATTCACGTCGGAGCAGCAGCACCGGAGATCCCAGAGGCGTTGATTGATCAGTTGAAGCC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G48330.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G48330.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G02810.1 (Glycine max), 3'ss of exon 3
----------------------gtgagcatcagttcaagtttttgagatttctttggtgtttctgtttttacattgctggtttcttgatggttttaa-aatagATGGGAGGCAAGGATGGGCTGAGTTTGCTCCGTATGATGCTATTCACGTCGGAGCAGCAGCACCGGAGATCCCAGAGGCGTTGATTGATCAGTTGAAGCC
|||| | | || || | | | |||||| || | || || || || | || ||| | | |||||| |||||||| ||| ||||||||||||| |||||||| |||||||| |||||||| ||||| || ||||| | | | ||||| |||||||||||
tgcatagctatattaatgtttcttgagaagtaaaataatttgctatg-tcaagttggtggatcaaatatttca--aatgtttgagtaattgttgtgttgacagATGGAAGGCAAGGTTGGCCTGAGTTTGCTCCTTATGATGCCATTCACGTTGGAGCAGCGGCACCCGAAATCCCCCAACCACTTATTGACCAGTTGAAGCC
upper sequence: AT3G48330.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA04G36430.1 (Glycine max), 3'ss of exon 3
--------------gtgagcatcagttcaagtttttga-----gatttctttggtgtttctgtttttacattgctggtttcttgatggttttaa-aatagATGGGAGGCAAGGATGGGCTGAGTTTGCTCCGTATGATGCTATTCACGTCGGAGCAGCAGCACCGGAGATCCCAGAGGCGTTGATTGATCAGTTGAAGCC
| | || | | | | | | | | | || | ||| | || | || ||| | || |||||| |||||||| ||| | |||||||| || |||||||| |||||||| |||||||||||||| || || || | | | ||||| |||||||||||
tgctaacaaaaactataacaattaatatttgctgataaaaaaaaaatgaacccatagttggaaccctggattagcagattgataattgttgtgttaacagATGGAAGGCAAGGTTGGCCAGAGTTTGCCCCTTATGATGCCATTCACGTTGGAGCAGCAGCACCAGAAATTCCCCAACCACTTATTGACCAGTTGAAGCC
upper sequence: AT3G48330.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA06G18460.1 (Glycine max), 3'ss of exon 5
------------------------------------------------------gtgagcatcagttcaagtttttgagatttctttggtgtttctgtttttacattg--ctggtttcttgatggttttaa----aatagATGGGAGGCAAGGATGGGCTGAGTTTGCTCCGTATGATGCTATTCACGTCGGAGCAGCAGCACCGGAGATCCCAGAGGCGTTGATTGATCAGTTGAAGCC
|| | | | | | || | || || ||| || || | | | ||||| || | | |||||| |||||||| ||| | |||||||| || |||||||| |||||||| |||||||||||||| || || || | | | ||||| |||||||||||
gtcatctgaaatctttcaatctgtgtgatattgtatacatcacaattgaatctaatggatagctgcatgattattgaacggttaaatgaatccatagttggaactctggattagcatattgataattgttgtgttgacagATGGAAGGCAAGGTTGGCCAGAGTTTGCACCTTATGATGCCATTCACGTTGGAGCAGCAGCACCAGAAATTCCCCAACCACTTATTGACCAGTTGAAGCC
upper sequence: AT3G48330.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv17s0000g09690.t01 (Vitis vinifera), 3'ss of exon 3
------------gtgagcatcagttcaagtttttgagatttctttggtgtttctgtttttacattgctggtttcttgatggttttaa--------aatagATGGGAGGCAAGGATGGGCTGAGTTTGCTCCGTATGATGCTATTCACGTCGGAGCAGCAGCACCGGAGATCCCAGAGGCGTTGATTGATCAGTTGAAGCC
| ||| ||| | | | || | | | || | || | ||| | | ||| || || |||||||| |||| ||| ||| |||||| ||| || |||||||| |||||||||||||| |||||||| ||||| ||| || | | |||||||||||||||||
aagtcgatgaaactagagatcttctcagggtataatcatggtgcttatttctccctccttttttctttggaatgctaatgattaaaattcatggtgatagATGGAAGGCTAGGTTGGCCTGAGTGTGCACCATATGATGCAATTCACGTCGGAGCCGCAGCACCTGAGATACCACAGCCACTTATTGATCAGTTGAAGCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttctttggtgtttctgtttttacattgctggtttcttgatggttttaaaatagATGGGAGGCAAGGATGGGCTGAGTTTGCTCCGTATGATGCTATTCACGTCGGAGCAGCAGCACCGGAGATCCCAGAGGCGTTGATTGATCAGTTGAAGCC
tcttgat putative branch site (score: 4)
atggttttaaaata TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagcatcagttcaagtttttgagatttctttggtgtttctgtttttacattgctggtttcttgatggttttaaaatagATGGGAGGCAAGGATGGGCTGAGTTTGCTCCGTATGATGCTATTCACGTCGGAGCAGCAGCACCGGAGATCCCAGAGGCGTTGATTGATCAGTTGAAGCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC